AMBER Archive (2009)

Subject: Re: [AMBER] How to derive charges from the output

From: bharat lakhani (lakhbharat_at_gmail.com)
Date: Tue Sep 01 2009 - 03:46:12 CDT

ok. accept this. There is no other way to derive charges from the gaussian
log file .As i described in my first mail. I am using these following
commands. when i am using these commands the resp_at.ac file showing the
charges also on metal ions. Is it working or showing some garbage value.
Thankyou sir

antechamber -i DRUG.log -fi gout -o $line.ac -fo ac
espgen -i DRUG.log -o $line.esp
respgen -i DRUG.ac -o $line.respin1 -f resp1
respgen -i DRUG.ac -o $line.respin2 -f resp2
resp -O -i DRUG.respin1 -o $line.respout1 -e $line.esp -t qout_stage1
resp -O -i DRUG.respin2 -o $line.respout2 -e $line.esp -q qout_stage1
-t qout_stage2
antechamber -i DRUG.ac -fi ac -o $line_resp.ac -fo ac -c rc -cf qout_stage2
atomtype -i DRUG_resp.ac -o *$line_resp_at.ac* -f ac -p amber
prepgen -i DRUG_resp_at.ac -o $line_int.prep -f int -rn SUS -rf SUS.res

On Tue, Sep 1, 2009 at 2:05 AM, FyD<fyd_at_q4md-forcefieldtools.org> wrote:
> Dear Florent & Bharat Lakhani,
>
>> Actually my output contains Fe-Porphrin with cysteine residue. when i
>> am runing this command it missing Fe as well as cysteine in the prein
>> file. Here i am attaching my gaussian log file and prepin file also.
>> Please let me know the proper way in order to calculate RESP fitting
>> charges on metal ions.
>
> Antechamber deals only with organic structures & is strongly connected to
> GAFF.
>
> Thus, you should try to use R.E.D. which handles metal complexes; FF
> libraries generated by R.E.D. can be used in association with various
force
> fields. There were several emails in the q4md-fft mailing list about metal
> complexes: I am sure you will find some of these emails useful.
>
> Finally, the prep.in force field libary format is more complex to
> understand. My feeling is that the Tripos2 mol2 file format is more
> intuitive and can be displayed in many graphical programs...
>
> regards, Francois
>
>
>
>> On Mon, Aug 31, 2009 at 1:08 PM, Barbault
>> Florent<florent.barbault_at_univ-paris-diderot.fr> wrote:
>>>
>>> Hello,
>>>
>>> I think there is a more simple way to do it. Personnaly, I use this
>>> command:
>>>
>>> antechamber -i gauss_output -fi gout -o prep.prepi -fo prepi -c resp -rn
>>> LIG
>>>
>>> Afterward, I reading the created file (prep.prepi) with an editor. Last
>>> column
>>> is the partial atomic charge derived with resp. You can also open this
>>> file
>>> with xleap in order to localize each atom with their respective charge.
>>>
>>> I hope this will help you.
>>> Regards,
>>> Florent Barbault
>>>
>>> Le lundi 31 août 2009, bharat lakhani a écrit :
>>>>
>>>> Respected sir,
>>>> I have GAUSSISN output log file. I want to
>>>> derive the partial charges from this log file. I am running these
>>>> following commands. Please suggest me.Is i am doing right or not. Its
>>>> very urgent.
>>>>
>>>>
>>>>
>>>> antechamber -i DRUG.log -fi gout -o $line.ac -fo ac
>>>> espgen -i DRUG.log -o $line.esp
>>>> respgen -i DRUG.ac -o $line.respin1 -f resp1
>>>> respgen -i DRUG.ac -o $line.respin2 -f resp2
>>>> resp -O -i DRUG.respin1 -o $line.respout1 -e $line.esp -t qout_stage1
>>>> resp -O -i DRUG.respin2 -o $line.respout2 -e $line.esp -q qout_stage1
>>>> -t qout_stage2
>>>> antechamber -i DRUG.ac -fi ac -o $line_resp.ac -fo ac -c rc -cf
>>>> qout_stage2
>>>> atomtype -i DRUG_resp.ac -o $line_resp_at.ac -f ac -p amber
>>>> prepgen -i DRUG_resp_at.ac -o $line_int.prep -f int -rn SUS -rf SUS.res
>>>>
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER_at_ambermd.org
>>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>> --
>>>
>>> -------------------------------------------------
>>> Dr Florent Barbault
>>> Maitre de conferences
>>> Universite Paris Diderot
>>> Laboratoire ITODYS
>>> 15 rue Jean de Baïf, bâtiment Lavoisier
>>> 75013 Paris FRANCE
>>> http://www.itodys.univ-paris7.fr/spip.php?article77
>>> tel : (33) 01-57-27-88-50
>>> e-mail : florent.barbault_at_univ-paris-diderot.fr
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>



_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber